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Hi Jie, the most obvious thing to do (and you might have tried that already) is to adjust the voxel size (in Å) and/or the contouring level of the map within Chimera. Both are normally associated with the EMDB entry of the map (under "map information”). Try to adjust these values in Chimera using the Volume Viewer menu. Good luck, Christian ________________________________ Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: [log in to unmask] Am 23.10.2014 um 19:45 schrieb jie liu <[log in to unmask]<mailto:[log in to unmask]>>: Dear you all May I ask a question? I tried to dock my protein structure onto an cryo-EM density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of the EM map region where the model is supposed to reside. I suspect the EM map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Your kind help is greatly appreciated! Jie